Emergence and increasing incidence of antibiotic resistant bacteria, makes it of great importance to discover the useful compounds to reduce diseases [1] and natural products have played a great role in discovery and development of new drugs. Thymus is one of the most important plants of lamiaceae family and the plant essence has been known to be microbicide. Since the endophytes residing in their host plants are able to produce the compounds similar to their host [2], in this study the bio effects of yeast and bacterial endophytes residing in Thymus were studied. During spring, summer and autumn of 2011, healthy Thymus plants were collected and 6 yeast and 23 bacterial endophytes were isolated from different parts of these plants. Bacterial strains were identified as Bacillus, Pseudomonas and Xanthomonas in which the Bacillus was the predominant one. Bioactivity of the endophytes were investigated against Botrytis cinerea, Xanthomonas arboricola pv. juglandis and Streptomyces scabies as plant pathogens and Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 33591 as human pathogenic bacteria. None of yeasts isolates had antifungal or antibacterial effects. Among bacterial strains, MB27 (Bacillus) showed the most antifungal effect against B. cinerea but there was no significant difference between this strain and MB12 (Bacillus). Out of 23 bacterial strains two strains, MB20 and MB27 (Bacillus), affected S. aureus and X. arboricola in which there were significant difference between them in both cases. MB20 and MB27 along with MB13 also prevented E. coli growth and there were significant difference at 1% level. None of bacterial endophytes affected S. scsbies. Growth inhibition mechanisms of endophytic bacteria were evaluated and it seems that their antimicrobial effects are related to production of protease enzyme, siderophore, hydrogen cyanide and volatile compounds. Regarding the results it is worthwhile that the plants with pharmaceutical history be conside
